refactor: remove FinnGenStepConfig

opentargets · Oct 25, 2023 · 2813fec · 2813fec
1 parent 5298e14
commit 2813fec
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Showing 5 changed files with 20 additions and 31 deletions.
diff --git a/config/step/my_finngen.yaml b/config/step/my_finngen.yaml
@@ -1,7 +1,4 @@
-# Default config
-defaults:
-  - finngen
-# Additional config
+_target_: otg.finngen.FinnGenStep
 finngen_phenotype_table_url: ${datasets.finngen_phenotype_table_url}
 finngen_release_prefix: ${datasets.finngen_release_prefix}
 finngen_sumstat_url_prefix: ${datasets.finngen_sumstat_url_prefix}

diff --git a/docs/python_api/step/finngen.md b/docs/python_api/step/finngen.md
@@ -1,4 +1,3 @@
 # FinnGen
 
 ::: otg.finngen.FinnGenStep
-::: otg.config.FinnGenStepConfig
diff --git a/src/otg/cli.py b/src/otg/cli.py
@@ -21,6 +21,7 @@ def main(cfg: Config) -> None:
     print(OmegaConf.to_yaml(cfg))
     # Instantiate ETL session
     session = instantiate(cfg.session)
+
     # Initialise and run step
     step = instantiate(cfg.step, session=session)
     step.run()

diff --git a/src/otg/config.py b/src/otg/config.py
@@ -257,28 +257,6 @@ class GWASCatalogSumstatsPreprocessConfig:
     study_id: str = MISSING
 
 
-@dataclass
-class FinnGenStepConfig:
-    """FinnGen study table ingestion step requirements.
-
-    Attributes:
-        finngen_phenotype_table_url (str): FinnGen API for fetching the list of studies.
-        finngen_release_prefix (str): Release prefix pattern.
-        finngen_sumstat_url_prefix (str): URL prefix for summary statistics location.
-        finngen_sumstat_url_suffix (str): URL prefix suffix for summary statistics location.
-        finngen_study_index_out (str): Output path for the FinnGen study index dataset.
-        finngen_summary_stats_out (str): Output path for the FinnGen summary statistics.
-    """
-
-    _target_: str = "otg.finngen.FinnGenStep"
-    finngen_phenotype_table_url: str = MISSING
-    finngen_release_prefix: str = MISSING
-    finngen_sumstat_url_prefix: str = MISSING
-    finngen_sumstat_url_suffix: str = MISSING
-    finngen_study_index_out: str = MISSING
-    finngen_summary_stats_out: str = MISSING
-
-
 @dataclass
 class UKBiobankStepConfig:
     """UKBiobank study table ingestion step requirements.
@@ -306,7 +284,6 @@ def register_configs() -> None:
     cs.store(name="v2g", group="step", node=V2GStepConfig)
     cs.store(name="colocalisation", group="step", node=ColocalisationStepConfig)
     cs.store(name="gwas_catalog", group="step", node=GWASCatalogStepConfig)
-    cs.store(name="finngen", group="step", node=FinnGenStepConfig)
     cs.store(name="ukbiobank", group="step", node=UKBiobankStepConfig)
     cs.store(
         name="gwas_catalog_sumstats_preprocess",

diff --git a/src/otg/finngen.py b/src/otg/finngen.py
@@ -6,14 +6,29 @@
 from urllib.request import urlopen
 
 from otg.common.session import Session
-from otg.config import FinnGenStepConfig
 from otg.datasource.finngen.study_index import FinnGenStudyIndex
 from otg.datasource.finngen.summary_stats import FinnGenSummaryStats
 
 
 @dataclass
-class FinnGenStep(FinnGenStepConfig):
-    """FinnGen ingestion step."""
+class FinnGenStep:
+    """FinnGen study table ingestion step requirements.
+
+    Attributes:
+        finngen_phenotype_table_url (str): FinnGen API for fetching the list of studies.
+        finngen_release_prefix (str): Release prefix pattern.
+        finngen_sumstat_url_prefix (str): URL prefix for summary statistics location.
+        finngen_sumstat_url_suffix (str): URL prefix suffix for summary statistics location.
+        finngen_study_index_out (str): Output path for the FinnGen study index dataset.
+        finngen_summary_stats_out (str): Output path for the FinnGen summary statistics.
+    """
+
+    finngen_phenotype_table_url: str
+    finngen_release_prefix: str
+    finngen_sumstat_url_prefix: str
+    finngen_sumstat_url_suffix: str
+    finngen_study_index_out: str
+    finngen_summary_stats_out: str
 
     session: Session = Session()